Napoleon instructed his commander, LeClerc to accommodate Toussaint and the black leaders until he got his army established. Then the black leaders were to be arrested, the black officers dismissed, and the black populace disarmed so that "special laws" -- meaning, according to James, slavery -- could be imposed. The plan required a lot of naivete on the part of the black revolutionary leaders, but excepting Toussaint, Dessalines, and a few others that expectation was well justified.
After Toussaint prevented Christophe from handing over Le Cap to the French, the battle for the town began on February 4th, 1802. The black army retreated, burning Le Cap behind them -- the beginning of a scorched earth policy that the island's defenders would pursue with vigor throughout the war.
Toussaint made little headway raising the mass of laborers, who were disillusion by his policies of accommodation with the white planters. Moreover, the officer's of the San Domingo army themselves vacillated in the face of French demands for submission, and several key positions, including the capital Port-Republicain, were surrendered without a fight.
In the West, Dessalines waged a campaign that combined audacious raids behind French lines with a fighting retreat, and also initiated his policy of massacring all the whites who fell in his hands.
The French tried to use Toussaint's sons to persuade him to give up, but to no avail.
Toussaint's strategy: use his smaller forces delay and harass the French until the rainy season without getting drawn into a decisive battle (with the wet weather would come disease that would deplete the French).
From mid-February, LeClerc's forces marched on Gonaives by converging routes. Christophe and Toussaint fought and orderly fighting retreat in the east, while Maurepas in the northwest and Dessalines in the south halted the French entirely. Just as the black masses were stirring to revolt in the north, however, Maurepas' was left exposed by the unexpected surrender of several of his subordinates who had been alienated by Toussaint's policy of destructive defense. Maurepas, too, submitted to preserve his position as a military leader. The French immediately put him to work leading the suppression of the revolt, with the added aim of undermining his credibility among the black masses.
As LeClerc prepared another offensive, this time aiming to converge on Verrettes, Toussaint struck out into the north to rally the laborers to revolt. He left Dessalines to hold the key fortress of Crete-a-Pierrot. The French suffered thousands of casualties attempting to seize the fort. Meanwhile, the political divide between the sides widened. Dessalines rallied his defenders behind a new cause: independence. French retaliation for Dessalines' massacres increasingly turned the black population in favor of revolt. Toussaint returned south to relieve the siege, but the black defenders broke out before he arrived.
With Crete-a-Pierrot subdued, LeClerc felt able to begin a crackdown on the mulattoes by deporting Rigaud. But Toussaint, hoping to secure a truce, refrained from seeking an alliance with the mulattoes. In the meantime, LeClerc received reinforcements and resumed the offensive against the rebel forces, but all of the French attacks were repulsed.
Toussaint still hoped for a favorable peace with the French, and began secret negotiations with LeClerc through Cristophe, one of his generals. Christophe's decision to surrender his forces -- accepting French guarantees to maintain black officers in their positions -- was a blow to the revolution and the negotiations. Toussaint persisted, however, and came to terms with LeClerc in late April on surrender with the same essential guarantee.
Though all Toussaint's commanders submitted to the deal, this was the key event that made Dessalines lose confidence in him. Dessalines began planning to lead a fight for independence himself. First, by suggesting that Toussaint was conspiring against the French, he goaded LeClerc into arresting and deporting him. This disposed of the only leader who could halt the momentum for Independence once fighting renewed.
In the wake of Toussaint's arrest, black laborers rebelled in some areas of the north, and these scattered rebellions spread and persisted thereafter. The black military leaders did not join the rebellions, and helped to contain them, but in the meantime the white French army was wasting away from disease. In late July, blacks in San Domingo received word that slavery had been reimposed in Guadeloupe, and the rebellions intensified, but the black generals still remained loyal to the French.
Finally, in October, 1802, first Petion, and then Clairveaux, Dessalines and Christophe, joined the rebellion with their troops. LeClrerc died at the beginning of November and was succeeded in French command by Rochambeau, who sought a more aggressive policy. He sought permission to restore slavery (not realizing that Napoleon had already authorized it to LeClerc). Once he received reinforcements, he went on the offensive and also started massacres of the mulattoes. This policy incited the mulatto-dominated South province to revolt. Meanwhile, Dessalines and Petion were bringing the local rebels under their control, training and imposing army discipline on them.
Toussaint died in a French prison in April, 1803.
In 1803, war had resumed in Europe. This was a turning point for the revolution, since there were no further reinforcements from the French, and the national army could buy all the arms it needed from the British. In November, the national army attacked Le Cap. The French fought off the attack. The battle convinced Rochambeau that the French position was too precarious to sustain, however, and he evacuated Le Cap.
On December 31st, the national leaders issued a declaration of Haitian independence. The following October, Dessalines declared himself emperor.
In early 1805, partly at the instigation of the British (who sought to stifle French trade), all the remaining whites in the country were massacred. In consequence, Haiti was isolated from the rest of the world for generations, and its development was stifled.